XLOC_009905


Basic Information

Item Value
gene id XLOC_009905
gene name NA
gene type non-coding
species zebrafish (Danio rerio)
category of species model fish

Chromosome Information

Item Value
chromosome id NC_007127.7
NCBI id CM002900.2
chromosome length 55266484
location 24565734 ~ 24573801 (+)
genome version GRCz11_2017_zebrafish_Genome

Sequence

>TCONS_00021714
TTATCAGAGGCTGCTTTGGGGCTCACATCATTCATTTGACCTGGCGTGGGAGCCGATAATCATAGACAGCAAAAGGGATTCTGACATGCACTTTCAGAAATCTCCGAAGGAAAAGGTGTGTTACCCTCTTCCCACAGTGAAGAAACTCCTGGAgcagaagagaaagagagaaacctCCACCTCAGCACCTCCATCCTGCTCGACAGCATCTTATACTGCTAGTGGAGCAGCTTCTGTCCCACAGGTGTTGGCATCAGTACAATCTCCTACAGCTGGAACCAGTGTAAGCTACACAGACATGGCAGCAGTTCGATACAACAGATGGGATGTTTCCAGCATTCATCAGCAGTGCAGCGCGTTCCCATTCATGTCCAGCTCTTCCAGCGCACCAAACTTTACTCAGACTGGACAGACACTTCCCAGTGCCTACAGCCCGCAGCAAATCCAAGACTGCCAGGATGCCCAGACAACACAGCTATACGTAAGAGCCACAGCAATGGTTCTCATTCTCattcacatatacagttgaagttagaattattagcccccctttgaatattattattattattattattattattaaatatttcccaaataaagtttttacagtatgtctgataatatttttcttctggagaatgtcttaattgttttatttcgactattaaaaaagcagttttaattaaaaaaaaaaaaaacattttaagggtaaaaataattagcccctttaagctatattttaagatctacagaacaaaccaccattatactctaacttgcctaattatcttaacctacctaattaatttaattaacctagttaagcctttaaattaccatttaggctgaatactagtgtcttgaaaaatatctagtgaaatattattgactgtcatcatggttGTTAGAgagaagttattaaaactattattctagaaattaagtttaaaaaaaaaaaaaaactctccgttaacagaaattaaaaaaaaaaaaaaaaaaaaaaaagggggctgttaattctgacttcaactgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatataaatatat
>TCONS_00021715
GCTGTTatatagttattagaaatgagttattaaaactattatgtttagaaatgtgttgaagaaatctgctctcggTTAAAGagaaaacagggaaaaaataaacagggggggctaataattctgacttcaactgtatgtaagtGTACGTGAGGAAGTTATGATCAtatattgtgtaaaataaaacaaaacaaaactaccagTCTGTTTTTTATTGAGCTCCATCAGATTAGGCATTTTACACCTATAGGAATCTTCTATTTTTGTTACTGTTGGATGCCATTCTTTCTAATGAAAGAATGGAATTAATGATTTAACCTCGAAAAAATAAGCACTACTTGAGGTGTGCTATATTTAACTTATCTTTACTATAATGTTCACAAATCTTCTTTGCCAAAAATGTTCTGAGTATTCAGAATAAATCCCAGTCTCCTGTACGTTATAGCTTCAGCAAAGAAAAAATCTGTTTCCCCAGCTCCGAAGGAAAAGGTGTGTTACCCTCTTCCCACAGTGAAGAAACTCCTGGAgcagaagagaaagagagaaacctCCACCTCAGCACCTCCATCCTGCTCGACAGCATCTTATACTGCTAGTGGAGCAGCTTCTGTCCCACAGGTGTTGGCATCAGTACAATCTCCTACAGCTGGAACCAGTGTAAGCTACACAGACATGGCAGCAGTTCGATACAACAGATGGGATGTTTCCAGCATTCATCAGCAGTGCAGCGCGTTCCCATTCATGTCCAGCTCTTCCAGCGCACCAAACTTTACTCAGACTGGACAGACACTTCCCAGTGCCTACAGCCCGCAGCAAATCCAAGACTGCCAGGATGCCCAGACAACACAGCTATACGTAAGAGCCACAGCAATGGTTCTCATTCTCattcacatatacagttgaagttagaattattagcccccctttgaatattattattattattattattattattaaatatttcccaaataaagtttttacagtatgtctgataatatttttcttctggagaatgtcttaattgttttatttcgactattaaaaaagcagttttaattaaaaaaaaaaaaaacattttaagggtaaaaataattagcccctttaagctatattttaagatctacagaacaaaccaccattatactctaacttgcctaattatcttaacctacctaattaatttaattaacctagttaagcctttaaattaccatttaggctgaatactagtgtcttgaaaaatatctagtgaaatattattgactgtcatcatggttGTTAGAgagaagttattaaaactattattctagaaattaagtttaaaaaaaaaaaaaaactctccgttaacagaaattaaaaaaaaaaaaaaaaaaaaaaaagggggctgttaattctgacttcaactgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtatatatatatatatatatatatatatatatatatataaatatat

Function

GO:

id name namespace
GO:0019219 regulation of nucleobase-containing compound metabolic process biological_process
GO:0019222 regulation of metabolic process biological_process
GO:0016070 RNA metabolic process biological_process
GO:0080090 regulation of primary metabolic process biological_process
GO:0018130 heterocycle biosynthetic process biological_process
GO:0006351 transcription, DNA-templated biological_process
GO:0006355 regulation of transcription, DNA-templated biological_process
GO:0006357 regulation of transcription by RNA polymerase II biological_process
GO:0051171 regulation of nitrogen compound metabolic process biological_process
GO:0006366 transcription by RNA polymerase II biological_process
GO:0090304 nucleic acid metabolic process biological_process
GO:0009059 macromolecule biosynthetic process biological_process
GO:0009889 regulation of biosynthetic process biological_process
GO:0097659 nucleic acid-templated transcription biological_process
GO:0031323 regulation of cellular metabolic process biological_process
GO:0031326 regulation of cellular biosynthetic process biological_process
GO:0051252 regulation of RNA metabolic process biological_process
GO:1903506 regulation of nucleic acid-templated transcription biological_process
GO:1901362 organic cyclic compound biosynthetic process biological_process
GO:0010467 gene expression biological_process
GO:0010468 regulation of gene expression biological_process
GO:0044271 cellular nitrogen compound biosynthetic process biological_process
GO:0060255 regulation of macromolecule metabolic process biological_process
GO:2001141 regulation of RNA biosynthetic process biological_process
GO:0032774 RNA biosynthetic process biological_process
GO:0019438 aromatic compound biosynthetic process biological_process
GO:0010556 regulation of macromolecule biosynthetic process biological_process
GO:0034645 cellular macromolecule biosynthetic process biological_process
GO:0034654 nucleobase-containing compound biosynthetic process biological_process
GO:2000112 regulation of cellular macromolecule biosynthetic process biological_process
GO:0005634 nucleus cellular_component
GO:0043565 sequence-specific DNA binding molecular_function
GO:0046872 metal ion binding molecular_function
GO:0003676 nucleic acid binding molecular_function
GO:0003677 DNA binding molecular_function
GO:0003690 double-stranded DNA binding molecular_function
GO:0003700 DNA-binding transcription factor activity molecular_function
GO:0000976 transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000977 RNA polymerase II transcription regulatory region sequence-specific DNA binding molecular_function
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific molecular_function
GO:0140110 transcription regulator activity molecular_function
GO:0043169 cation binding molecular_function
GO:0001067 regulatory region nucleic acid binding molecular_function
GO:1990837 sequence-specific double-stranded DNA binding molecular_function

KEGG:

id description
ko03230 Viral genome structure
ko05164 Influenza A
ko03200 Viral proteins

RNA

RNA id representative length rna type GC content exon number start site end site
TCONS_00021714 False 1126 lncRNA 0.36 4 24565734 24573801
TCONS_00021715 True 1497 lncRNA 0.34 3 24572141 24573801

Neighbor

gene id symbol gene type direction distance location
XLOC_009904 CT867948.1 coding upstream 41658 24516092 ~ 24524076 (+)
XLOC_009903 NA coding upstream 357831 24198479 ~ 24207903 (+)
XLOC_009902 NA coding upstream 537116 24019108 ~ 24028618 (+)
XLOC_009901 apoc2 coding upstream 571092 23984179 ~ 23994642 (+)
XLOC_009900 apoa2 coding upstream 585380 23978978 ~ 23980354 (+)
XLOC_009906 si:dkey-56f14.7 coding downstream 52647 24626448 ~ 24646067 (+)
XLOC_009907 ywhabl coding downstream 107376 24681177 ~ 24695891 (+)
XLOC_009908 smg9 coding downstream 147755 24721556 ~ 24733321 (+)
XLOC_009909 si:dkey-79d12.4 coding downstream 159940 24733741 ~ 24741400 (+)
XLOC_009910 NA coding downstream 260974 24834775 ~ 24897111 (+)
XLOC_009889 CR533578.1 non-coding upstream 958382 23607231 ~ 23607352 (+)
XLOC_009875 NA non-coding upstream 1869238 22695226 ~ 22696496 (+)
XLOC_009911 dre-let-7d-1 non-coding downstream 307321 24881122 ~ 24881218 (+)
XLOC_009912 dre-mir-125a-1 non-coding downstream 324370 24898171 ~ 24898253 (+)
XLOC_009913 BX539313.2 non-coding downstream 331755 24905556 ~ 24918957 (+)
XLOC_009929 NA non-coding downstream 633817 25207618 ~ 25213978 (+)

Expression


Co-expression Network

Homologous

species gene id symbol gene type chromosome NCBI id location
grasscarp (Ctenopharyngodon idella) CI01000027_05398796_05408689 NA coding CI01000027 null 5398408 ~ 5410067 (+)
grasscarp (Ctenopharyngodon idella) G146652 NA non-coding CI01000028 null 3483447 ~ 3483716 (+)